Build branch main with version main (38f635a)
Build pipeline: viash-hub.biobox.main-dz9k8
Source commit: 38f635ad57
Source message: Add agat convert genscan2gff (#100)
* add config
* add help
* add test data and expected output adn the script to obtain them
* add running script
* add test script
* update changelog
* cleanup
* fix tests
* format description
* remove unused argument --inflate-off
* update --config description
* add requirements
* create temporary directory and clean up on exit
* add GENSCAN in keywords
* add set -e to test
* fix create temporary directory
* add set -eo pipefail to test
* add set -eo pipefail to script
* fix create temporary directory
* update --config description
* cleanup changelog
* cleanup changelog
* Update deprecated variable
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
This commit is contained in:
@@ -610,15 +610,16 @@ build_info:
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engine: "docker|native"
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output: "target/executable/umi_tools/umi_tools_dedup"
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executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup"
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viash_version: "0.9.0-RC7"
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git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
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git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
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viash_version: "0.9.0"
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git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
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git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
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git_tag: "v0.2.0-2-g38f635a"
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package_config:
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name: "biobox"
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version: "main"
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description: "A collection of bioinformatics tools for working with sequence data.\n"
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info: null
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viash_version: "0.9.0-RC7"
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viash_version: "0.9.0"
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source: "src"
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target: "target"
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config_mods:
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@@ -2,9 +2,9 @@
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# umi_tools_dedup main
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#
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# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
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# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
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# Data Intuitive.
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# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# Intuitive.
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#
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# The component may contain files which fall under a different license. The
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# authors of this component should specify the license in the header of such
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@@ -770,9 +770,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
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LABEL org.opencontainers.image.authors="Emma Rousseau"
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LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
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LABEL org.opencontainers.image.created="2024-09-16T07:55:09Z"
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LABEL org.opencontainers.image.created="2024-09-17T06:47:27Z"
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LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
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LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
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LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
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LABEL org.opencontainers.image.version="main"
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VIASHDOCKER
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@@ -448,15 +448,16 @@ build_info:
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engine: "docker|native"
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output: "target/executable/umi_tools/umi_tools_extract"
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executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract"
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viash_version: "0.9.0-RC7"
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git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
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git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
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viash_version: "0.9.0"
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git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
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git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
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git_tag: "v0.2.0-2-g38f635a"
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package_config:
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name: "biobox"
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version: "main"
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description: "A collection of bioinformatics tools for working with sequence data.\n"
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info: null
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viash_version: "0.9.0-RC7"
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viash_version: "0.9.0"
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source: "src"
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target: "target"
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config_mods:
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@@ -2,9 +2,9 @@
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# umi_tools_extract main
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#
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# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
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# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
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# Data Intuitive.
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# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# Intuitive.
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#
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# The component may contain files which fall under a different license. The
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# authors of this component should specify the license in the header of such
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@@ -637,9 +637,9 @@ ENTRYPOINT []
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RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
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LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract"
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LABEL org.opencontainers.image.created="2024-09-16T07:55:08Z"
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LABEL org.opencontainers.image.created="2024-09-17T06:47:26Z"
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LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
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LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
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LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
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LABEL org.opencontainers.image.version="main"
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VIASHDOCKER
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@@ -255,15 +255,16 @@ build_info:
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engine: "docker|native"
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output: "target/executable/umi_tools/umi_tools_prepareforrsem"
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executable: "target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem"
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viash_version: "0.9.0-RC7"
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git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
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git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
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viash_version: "0.9.0"
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git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
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git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
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git_tag: "v0.2.0-2-g38f635a"
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package_config:
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name: "biobox"
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version: "main"
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description: "A collection of bioinformatics tools for working with sequence data.\n"
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info: null
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viash_version: "0.9.0-RC7"
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viash_version: "0.9.0"
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source: "src"
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target: "target"
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config_mods:
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@@ -2,9 +2,9 @@
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# umi_tools_prepareforrsem main
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#
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# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
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# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
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# Data Intuitive.
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# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# Intuitive.
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#
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# The component may contain files which fall under a different license. The
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# authors of this component should specify the license in the header of such
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@@ -519,9 +519,9 @@ ENTRYPOINT []
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RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
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LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_prepareforrsem"
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LABEL org.opencontainers.image.created="2024-09-16T07:55:09Z"
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LABEL org.opencontainers.image.created="2024-09-17T06:47:26Z"
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LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
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LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
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LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
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LABEL org.opencontainers.image.version="main"
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VIASHDOCKER
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